Skip to main content
SpringerLink
Log in

Sequencing consolidates molecular markers with plant breeding practice

  • Review
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Key message

Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding.

Abstract

The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Akfirat FS, Ertugrul F, Hasancebi S et al (2013) Chromosomal location of genomic SSR markers associated with yellow rust resistance in Turkish bread wheat (Triticum aestivum L.). J Genet 92:233–240

    PubMed  Google Scholar 

  • Andolfatto P, Davison D, Erezyilmaz D et al (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 21:610–617

    PubMed Central  CAS  PubMed  Google Scholar 

  • Antony G, Zhou J, Huang S et al (2010) Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3. Plant Cell 22:3864–3876

    PubMed Central  CAS  PubMed  Google Scholar 

  • Atwell S, Huang YS, Vilhjálmsson BJ et al (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631

    PubMed Central  CAS  PubMed  Google Scholar 

  • Baird NA, Etter PD, Atwood TS et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376

    PubMed Central  PubMed  Google Scholar 

  • Barchi L, Lanteri S, Portis E et al (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12:304

    PubMed Central  CAS  PubMed  Google Scholar 

  • Boersma JG, Buirchell BJ, Sivasithamparam K, Yang H (2007a) Development of a PCR marker tightly linked to mollis, the gene that controls seed dormancy in Lupinus angustifolius L. Plant Breed 126:612–616

    CAS  Google Scholar 

  • Boersma JG, Buirchell BJ, Sivasithamparam K, Yang H (2007b) Development of two sequence-specific PCR markers linked to the le gene that reduces pod shattering in narrow-leafed Lupin (Lupinus angustifolius L.). Genet Mol Biol 30:623–629

    CAS  Google Scholar 

  • Boersma J, Nelson M, Sivasithamparam K, Yang H (2009) Development of sequence-specific PCR markers linked to the Tardus gene that reduces pod shattering in narrow-leafed lupin (Lupinus angustifolius L.). Mol Breed 23:259–267

    CAS  Google Scholar 

  • Brenchley R, Spannagl M, Pfeifer M et al (2013) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705–710

    Google Scholar 

  • Brien SJ, A CW, Potter RH et al (1999) A molecular marker for early maturity (Ku) and marker-assisted breeding of Lupinus angustifolius. In: Proceedings of the 9th international lupin conference, Klink/Muritz, Germany, pp 115–117

  • Brumlop S, Finckh MR (2011) Applications and potentials of marker assisted selection (MAS) in plant breeding. BundesamtfürNaturschutz (BfN), Bonn, Germany

  • Brunner S, Hurni S, Streckeisen P et al (2010) Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles. Plant J 64:433–445

    CAS  PubMed  Google Scholar 

  • Bus A, Hecht J, Huettel B et al (2012) High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics 13:281

    PubMed Central  CAS  PubMed  Google Scholar 

  • Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11:215–221

    PubMed  Google Scholar 

  • Chen W, Sun L, Zhao F et al (2012) The genome of Prunus mume. Nat Commun 3:1318

  • Chen J, Huang Q, Gao D et al (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun 4:1595–1599

    PubMed Central  PubMed  Google Scholar 

  • Cheng SH, Cao LY, Yang SH, Zhai HQ (2004) Forty years’ development of hybrid rice: China’s experience. Rice Sci 11:225–230

    Google Scholar 

  • Chia J-M, Song C, Bradbury PJ et al (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44:803–807

    CAS  PubMed  Google Scholar 

  • Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A et al (2011) Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. BMC Genomics 12:4

    PubMed Central  CAS  PubMed  Google Scholar 

  • Clements JC, Dracup M, Buirchell BJ, Smith CG (2005) Variation for seed coat and pod wall percentage and other traits in a germplasm collection and historical cultivars of lupins. Aust J Agric Res 56:75–83

    Google Scholar 

  • Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B: Biol Sci 363:557–572

    CAS  Google Scholar 

  • Connelly CF, Akey JM (2012) On the prospects of whole-genome association mapping in Saccharomyces cerevisiae. Genetics 191:1345–1353

    PubMed Central  CAS  PubMed  Google Scholar 

  • Cowling WA, Hamblin J, Wood PM, Gladstones JS (1987) Resistance to Phomopsis stem blight in Lupinus angustifolius L. Crop Sci 27:648–652

    Google Scholar 

  • Dai F, Nevo E, Wu D et al (2012) Tibet is one of the centers of domestication of cultivated barley. Proc Natl Acad Sci USA 109:16969–16973

    PubMed Central  CAS  PubMed  Google Scholar 

  • Davey JW, Hohenlohe PA, Etter PD et al (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510

    CAS  PubMed  Google Scholar 

  • Desta ZA, Ortiz R (2014) Genomic selection: genome-wide prediction in plant improvement. Trends Plant Sci 19:592–601

    CAS  PubMed  Google Scholar 

  • Ellis JG, Lagudah ES, Spielmeyer W, Dodds PN (2014) The past, present and future of breeding rust resistant wheat. Front Plant Sci 5:641

    PubMed Central  PubMed  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    PubMed Central  CAS  PubMed  Google Scholar 

  • Emerson KJ, Merz CR, Catchen JM et al (2010) Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci USA 107:16196–16200

    PubMed Central  CAS  PubMed  Google Scholar 

  • Etter PD, Preston JL, Bassham S et al (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS One 6:e18561

    PubMed Central  CAS  PubMed  Google Scholar 

  • Evans DE, Li C, Eglinton JK (2010) The properties and genetics of barley malt starch degrading enzymes. In: Zhang G, Li C (eds) Advanced topics in science and technology in China. Springer, Berlin, pp 143–189

    Google Scholar 

  • Feuillet C, Leach JE, Rogers J et al (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77–88

    CAS  PubMed  Google Scholar 

  • Francki MG, Mullan DJ (2004) Application of comparative genomics to narrow-leafed lupin (Lupinus angustifolius L.) using sequence information from soybean and Arabidopsis. Génome 47:623–632

    CAS  PubMed  Google Scholar 

  • Gao Z-Y, Zhao S-C, He W-M et al (2013) Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Proc Natl Acad Sci USA 110:14492–14497

    PubMed Central  CAS  PubMed  Google Scholar 

  • Gebhardt C (2013) Bridging the gap between genome analysis and precision breeding in potato. Trends Genet 29:248–256

    CAS  PubMed  Google Scholar 

  • Goettel W, Xia E, Upchurch R et al (2014) Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content. BMC Genomics 15:299

    PubMed Central  PubMed  Google Scholar 

  • Goff SA, Ricke D, Lan T-H et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    CAS  PubMed  Google Scholar 

  • Gore MA, Chia JM, Elshire RJ et al (2009) A first-generation haplotype map of maize. Science 326:1115–1117

    CAS  PubMed  Google Scholar 

  • Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18

    CAS  PubMed  Google Scholar 

  • Hayden MJ, Kuchel H, Chalmers KJ (2004) Sequence tagged microsatellites for the Xgwm533 locus provide new diagnostic markers to select for the presence of stem rust resistance gene Sr2 in bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1641–1647

    CAS  PubMed  Google Scholar 

  • He XY, He ZH, Zhang LP et al (2007) Allelic variation of polyphenol oxidase (PPO) genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat. Theor Appl Genet 115:47–58

    CAS  PubMed  Google Scholar 

  • Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1

    CAS  Google Scholar 

  • Huang X, Feng Q, Qian Q et al (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076

    PubMed Central  CAS  PubMed  Google Scholar 

  • Hufford MB, Xu X, van Heerwaarden J et al (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44:808–811

    CAS  PubMed  Google Scholar 

  • Hyten DL, Cannon SB, Song Q et al (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38

    PubMed Central  PubMed  Google Scholar 

  • International Peach Genome Initiative, Verde I, Abbott AG et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494

    Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Google Scholar 

  • Iyer-Pascuzzi A, McCouch S (2007) Functional markers for xa5-mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296

    CAS  Google Scholar 

  • Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177

    CAS  PubMed  Google Scholar 

  • Jia J, Zhao S, Kong X et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95

    CAS  PubMed  Google Scholar 

  • Jiao Y, Zhao H, Ren L et al (2012) Genome-wide genetic changes during modern breeding of maize. Nat Genet 44:812–815

    CAS  PubMed  Google Scholar 

  • Juwattanasomran R, Somta P, Kaga A et al (2012) Identification of a new fragrance allele in soybean and development of its functional marker. Mol Breed 29:13–21

    CAS  Google Scholar 

  • Kim MY, Lee S, Van K et al (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107:22032–22037

    PubMed Central  CAS  PubMed  Google Scholar 

  • Kroc M, Koczyk G, Swiecicki W et al (2014) New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin). Theor Appl Genet 127:1237–1249

    PubMed  Google Scholar 

  • Kumar S, You FM, Cloutier S (2012) Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries. BMC Genomics 13:684–694

    PubMed Central  CAS  PubMed  Google Scholar 

  • Li R, Zhu H, Ruan J et al (2010a) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272

    PubMed Central  CAS  PubMed  Google Scholar 

  • Li X, Renshaw D, Yang H, Yan G (2010b) Development of a co-dominant DNA marker tightly linked to gene tardus conferring reduced pod shattering in narrow-leafed lupin (Lupinus angustifolius L.). Euphytica 176:49–58

    CAS  Google Scholar 

  • Li X, Yang H, Buirchell B, Yan G (2011) Development of a DNA marker tightly linked to low-alkaloid gene iucundus in narrow-leafed lupin (Lupinus angustifolius L.) for marker-assisted selection. Crop Pasture Sci 62:218–224

    CAS  Google Scholar 

  • Li X, Buirchell B, Yan G, Yang H (2012a) A molecular marker linked to the mollis gene conferring soft-seediness for marker-assisted selection applicable to a wide range of crosses in lupin (Lupinus angustifolius L.) breeding. Mol Breed 29:361–370

    Google Scholar 

  • Li X, Yang H, Yan G (2012b) Development of a co-dominant DNA marker linked to the gene lentus conferring reduced pod shattering for marker-assisted selection in narrow-leafed lupin (Lupinus angustifolius) breeding. Plant Breed 131:540–544

    CAS  Google Scholar 

  • Li Y-H, Zhao S-C, Ma J-X et al (2013) Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 14:579

    PubMed Central  PubMed  Google Scholar 

  • Li Z, Fu B-Y, Zhang G, McNally KL (2014) The 3,000 rice genomes project. GigaScience 3:1–6

    Google Scholar 

  • Lin T, Zhu G, Zhang J et al (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220–1226

    CAS  PubMed  Google Scholar 

  • Ling H-Q, Zhao S, Liu y et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90

    CAS  PubMed  Google Scholar 

  • Lorenz AJ, Chao S, Asoro FG et al (2011) Genomic selection in plant breeding. In: Sparks DL (eds) Advances in agronomy. Elsevier, pp 77–123

  • Ma J, Yan GJ, Liu CJ (2011) Development of near-isogenic lines for a major QTL on 3BL conferring Fusarium crown rot resistance in hexaploid wheat. Euphytica 183:147–152

    Google Scholar 

  • Mammadov J, Chen W, Ren R et al (2010) Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding. Theor Appl Genet 121:577–588

    CAS  PubMed  Google Scholar 

  • Miller MR, Dunham JP, Amores A et al (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248

    PubMed Central  CAS  PubMed  Google Scholar 

  • Molina J, Sikora M, Garud N et al (2011) Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci USA 108:8351–8356

    PubMed Central  CAS  PubMed  Google Scholar 

  • Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977

    PubMed Central  CAS  PubMed  Google Scholar 

  • Morris GP, Ramu P, Deshpande SP et al (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci USA 110:453–458

    PubMed Central  CAS  PubMed  Google Scholar 

  • Mortimer SA, Kidwell MA, Doudna JA (2014) Insights into RNA structure and function from genome-wide studies. Nat Rev Genet 15:469–479

    CAS  PubMed  Google Scholar 

  • Nakaya A, Isobe SN (2012) Will genomic selection be a practical method for plant breeding? Ann Bot 110:1303–1316

    PubMed Central  PubMed  Google Scholar 

  • Nelson MN, Phan HTT, Ellwood SR et al (2006) The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula. Theor Appl Genet 113:225–238

    CAS  PubMed  Google Scholar 

  • Nelson MN, Moolhuijzen PM, Boersma JG et al (2010) Aligning a new reference genetic map of Lupinus angustifolius with the genome sequence of the model legume, Lotus japonicus. DNA Res 17:73–83

    PubMed Central  CAS  PubMed  Google Scholar 

  • Nicolai M, Pisani C, Bouchet J-P et al (2012) Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum). Genet Mol Res 11:2295–2300

    CAS  PubMed  Google Scholar 

  • Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12:443–451

    PubMed Central  CAS  PubMed  Google Scholar 

  • Nielsen R, Korneliussen T, Albrechtsen A et al (2012) SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLoS One 7:e37558

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ogbonnaya FC, Subrahmanyam NC, Moullet O et al (2001) Diagnostic DNA markers for cereal cyst nematode resistance in bread wheat. Aust J Agric Res 52:1367–1374

    CAS  Google Scholar 

  • Park C-J, Ronald PC (2012) Cleavage and nuclear localization of the rice XA21 immune receptor. Nat Commun 3:920

    PubMed Central  PubMed  Google Scholar 

  • Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556

    CAS  PubMed  Google Scholar 

  • Pérez-de-Castro AM, Vilanova S, Cañizares J et al (2012) Application of genomic tools in plant breeding. Curr Genomics 13:179–195

    PubMed Central  PubMed  Google Scholar 

  • Poland J, Endelman J, Dawson J et al (2012a) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113

    CAS  Google Scholar 

  • Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012b) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253

    PubMed Central  CAS  PubMed  Google Scholar 

  • Qi J, Liu X, Shen D et al (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45:1510–1515

    CAS  PubMed  Google Scholar 

  • Qi X, Li M-W, Xie M et al (2014) Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun 5:4340

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ramirez-Gonzalez RH, Segovia V, Bird N et al (2014) RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnol J. doi:10.1111/pbi.12281

    PubMed  Google Scholar 

  • Rex B, Yu J (2007) Prospects for genome-wide selection for quantitative traits in maize. Crop Sci 47:1082–1090

    Google Scholar 

  • Ribaut J-M, de Vicente MC, Delannay X (2010) Molecular breeding in developing countries: challenges and perspectives. Curr Opin Plant Biol 13:213–218

    PubMed  Google Scholar 

  • Sahu BB, Sumit R, Srivastava SK, Bhattacharyya MK (2012) Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome. BMC Genomics 13:20

    PubMed Central  CAS  PubMed  Google Scholar 

  • Saintenac C, Jiang D, Wang S, Akhunov E (2013) Sequence-based mapping of the polyploid wheat genome. G3 (Bethesda) 3:1105–1114

    Google Scholar 

  • Schaeffer LR (2006) Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet 123:218–223

    CAS  PubMed  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

    CAS  PubMed  Google Scholar 

  • Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115

    CAS  PubMed  Google Scholar 

  • Shahidul I, Yang H, Yan G (2013) Molecular markers for genetics and plant breeding: the MFLP marker system and its application in narrow-leafed lupin (Lupinus angustifolius). Methods Mol Biol 1069:179–201

    CAS  PubMed  Google Scholar 

  • Shankar M, Cowling WA, Sweetingham M (1996) The expression of resistance to latent stem infection by Diaporthe toxica in narrow-leafed lupin. Phytopathology 86:692–697

    Google Scholar 

  • Sharp PJ, Johnston S, Brown G et al (2001) Validation of molecular markers for wheat breeding. Aust J Agric Res 52:1357–1366

    CAS  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Google Scholar 

  • The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716

    Google Scholar 

  • The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768

    Google Scholar 

  • The International Wheat Genome Sequencing Consortium (IWGSC), Mayer KFX, Rogers J et al (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788

    Google Scholar 

  • Uitdewilligen JG, Wolters A-MA, Bjorn B et al (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One 8:e62355

    PubMed Central  CAS  PubMed  Google Scholar 

  • Vales M, Dossmann J, Delgado D, Duque MC (2009) Parallel and interlaced recurrent selection (PAIRS): demonstration of the feasibility of implementing PAIRS to improve complete and partial resistance to blast (Magnaporthe grisea) and some other main traits in rice. Field Crops Res 111:173–178

    Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630

    CAS  PubMed  Google Scholar 

  • Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530

    CAS  PubMed  Google Scholar 

  • Varshney RK, Chen W, Li Y et al (2012a) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30:83–89

    CAS  Google Scholar 

  • Varshney RK, Ribaut J-M, Buckler ES et al (2012b) Can genomics boost productivity of orphan crops? Nat Biotechnol 30:1172–1176

    CAS  PubMed  Google Scholar 

  • Varshney RK, Song C, Saxena RK et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246

    CAS  PubMed  Google Scholar 

  • Velasco R, Zharkikh A, Affourtit J et al (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839

    CAS  PubMed  Google Scholar 

  • Wang X, Wang H, Wang J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039

    CAS  PubMed  Google Scholar 

  • Wang XQ, Zhao L, Eaton DAR et al (2013) Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing. Mol Ecol Resour 13:938–945

    CAS  PubMed  Google Scholar 

  • Ward JA, Bhangoo J, Fernández-Fernández F et al (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14:2–15

    PubMed Central  CAS  PubMed  Google Scholar 

  • Williamson PM, Sivasithamparam K, Cowling WA (1991) Formation of subcuticular hyphae by Phomopsis leptostromiformis upon latent infection of narrow-leafed lupins. Plant Dis 75:1023–1025

    Google Scholar 

  • Willing E-M, Hoffmann M, Klein JD et al (2011) Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics 27:2187–2193

    CAS  PubMed  Google Scholar 

  • Wolko B, Weeden NF (1994) Linkage map of isozyme and RAPD markers for the Lupinus angustifolius L. ISA Press, Lisbon, pp 42–49

    Google Scholar 

  • Xu Y (2010) Molecular plant breeding. CABI, Wallingford, pp 1–755

    Google Scholar 

  • Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407

    Google Scholar 

  • Xu X, Pan S, Cheng S et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195

    CAS  PubMed  Google Scholar 

  • Xu Y, Lu Y, Xie C et al (2012) Whole-genome strategies for marker-assisted plant breeding. Mol Breed 29:833–854

    Google Scholar 

  • Xu Y, Xie C, Wan J et al (2013) Marker-assisted selection in cereals: platforms, strategies and examples. In: Gupta PK, Varshney RK (eds) Cereal genomics II. Springer, Netherlands, pp 375–411

    Google Scholar 

  • Yagi M, Kosugi S, Hirakawa H et al (2014) Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). DNA Res 21:231–241

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yang H, Sweetingham MW, Cowling WA, Smith PM (2001) DNA fingerprinting based on microsatellite-anchored fragment length polymorphisms, and isolation of sequence-specific PCR markers in lupin (Lupinus angustifolius L.). Mol Breed 7:203–209

    Google Scholar 

  • Yang H, Shankar M, Buirchell BJ et al (2002) Development of molecular markers using MFLP linked to a gene conferring resistance to Diaporthe toxica in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet 105:265–270

    CAS  PubMed  Google Scholar 

  • Yang H, Boersma JG, You M et al (2004) Development and implementation of a sequence-specific PCR marker linked to a gene conferring resistance to anthracnose disease in narrow-leafed lupin (Lupinus angustifolius L.). Mol Breed 14:145–151

    CAS  Google Scholar 

  • Yang H, Renshaw D, Thomas G et al (2008) A strategy to develop molecular markers applicable to a wide range of crosses for marker assisted selection in plant breeding: a case study on anthracnose disease resistance in lupin (Lupinus angustifolius L.). Mol Breed 21:473–483

    Google Scholar 

  • Yang H, Lin R, Renshaw D et al (2010) Development of sequence-specific PCR markers associated with a polygenic controlled trait for marker-assisted selection using a modified selective genotyping strategy: a case study on anthracnose disease resistance in white lupin (Lupinus albus L.). Mol Breed 25:239–249

    CAS  Google Scholar 

  • Yang H, Tao Y, Zheng Z et al (2012) Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics 13:318–328

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yang H, Tao Y, Zheng Z et al (2013a) Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding. Theor Appl Genet 126:511–522

    CAS  PubMed  Google Scholar 

  • Yang H, Tao Y, Zheng Z et al (2013b) Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L. PLoS One 8:e64799

    PubMed Central  CAS  PubMed  Google Scholar 

  • You M, Boersma JG, Buirchell BJ et al (2005) A PCR-based molecular marker applicable for marker-assisted selection for anthracnose disease resistance in lupin breeding. Cell Mol Biol Lett 10:123–134

    CAS  PubMed  Google Scholar 

  • Young ND, Debellé F, Oldroyd GED et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    CAS  PubMed  Google Scholar 

  • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    PubMed Central  CAS  PubMed  Google Scholar 

  • Zhang D, Song H, Cheng H et al (2014) The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. PLoS Genet 10:e1004061

    PubMed Central  PubMed  Google Scholar 

  • Zheng Z, Wang HB, Chen GD, Yan GJ, Liu CJ (2013) A procedure allowing up to eight generations of wheat and nine generations of barley per annum. Euphytica 191:311–316

    Google Scholar 

  • Zhou L, Chen Z, Lang X et al (2013) Development and validation of a PCR-based functional marker system for the brown planthopper resistance gene Bph14 in rice. Breed Sci 63:347–352

    PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We greatly appreciate the two anonymous reviewers for their invaluable comments and suggestions. The research is supported by the Western Australian Government through the Lupin Molecular Marker Strategy Project to H. Y.; and the Hong Kong RGC Collaborative Research Fund (CUHK3/CRF/11G) and the Hong Kong RGC General Research Fund (468610) to H. M. L.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia

    Huaan Yang, Chengdao Li & Jonathan Clements

  2. State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia

    Chengdao Li

  3. Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

    Hon-Ming Lam & Shancen Zhao

  4. Faculty of Sciences and The UWA Institute of Agriculture, School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia

    Guijun Yan

  5. BGI-Shenzhen, Shenzhen, 518083, China

    Shancen Zhao

Authors
  1. Huaan Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chengdao Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hon-Ming Lam
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jonathan Clements
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Guijun Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shancen Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Huaan Yang or Shancen Zhao.

Additional information

Communicated by R. K. Varshney.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yang, H., Li, C., Lam, HM. et al. Sequencing consolidates molecular markers with plant breeding practice. Theor Appl Genet 128, 779–795 (2015). https://doi.org/10.1007/s00122-015-2499-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-015-2499-8

Keywords

Search

Navigation